[Bioc-devel] Patch for Biostrings::letterFrequencyInSlidingView over XStringSet

[Steve Lianoglou]

Hi,

I recently needed to have letterFrequencyInSlidingView work on
multiple strings at once.

I initially iterated over my XStringSet in R and passed each element
to the letterFrequencyInSlidingView method, but this was really slow
over large XStringSet objects.

I bit the bullet and wrote the loop in C as the
"XStringSet_letterFrequencyInSlidingView" you'll see defined in this
diff.

That function basically calls a slightly modified
XString_letterFrequencyInSlidingView, which is also added as
_XString_letterFrequencyInSlidingView.

Slight changes to the documentation, etc. is also included in this
patch, which is against svn revision 52588, in order to make it "well
rounded."

If the "powers that be" deem this a worthy addition, could you please
apply this, or some cleaned version of it? This was my first real
foray into modifying any C code in these large/well-established
libraries, so ... I did a bit of hunting and pecking, and you'll
surely have an opinion of how to do it better.

The way it is implemented now, the
XString_letterFrequencyInSlidingView is no longer being called
directly and I guess should be removed if this is the appropriate
style. The XStringSet_letterFrequencyInSlidingView is always delegated
to, in a similar way that there is only a XStringSet_letterFrequency ,
and no XString_letterFrequency.

The patch is attached.

If attachments don't come through (can't remember if they get
stripped), you can also find it here:
http://cbio.mskcc.org/~lianos/files/bioconductor/biostrings.diff

Thanks,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact